RSRC1

arginine and serine rich coiled-coil 1

Basic information

Region (hg38): 3:158105855-158545730

Links

ENSG00000174891 ∙ NCBI:51319 ∙ OMIM:613352 ∙ HGNC:24152 ∙ Uniprot:Q96IZ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder, autosomal recessive 70 (Moderate), mode of inheritance: AR
• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
• intellectual developmental disorder, autosomal recessive 70 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual development disorder, autosomal recessive 70	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	28640246; 29522154

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RSRC1 gene.

• Inborn genetic diseases (2 variants)
• Intellectual developmental disorder, autosomal recessive 70 (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RSRC1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			23	1	1	25
nonsense	2					2
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)	2	1				3
splice region						0
non coding						0
Total	4	2	23	2	1

Highest pathogenic variant AF is 0.0000263

Variants in RSRC1

This is a list of pathogenic ClinVar variants found in the RSRC1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-158105856-G-C		not specified	Uncertain significance (May 30, 2023)
3-158105871-T-C		not specified	Uncertain significance (May 14, 2024)
3-158105889-C-G		not specified	Likely benign (Apr 07, 2023)
3-158105894-G-C		not specified	Uncertain significance (Jan 23, 2024)
3-158105895-T-C		not specified	Likely benign (Apr 07, 2023)
3-158105897-C-T		not specified	Uncertain significance (Apr 07, 2023)
3-158105910-C-G		not specified	Uncertain significance (Jul 14, 2023)
3-158105962-C-T		SHOX2-related disorder	Likely benign (Jul 24, 2019)
3-158106011-G-T		not specified	Uncertain significance (Aug 13, 2021)
3-158122107-G-T		Intellectual developmental disorder, autosomal recessive 70	Pathogenic (Feb 14, 2022)
3-158122114-C-T		Inborn genetic diseases	Uncertain significance (Sep 27, 2022)
3-158122115-G-A		Intellectual developmental disorder, autosomal recessive 70	Uncertain significance (Feb 19, 2021)
3-158122166-G-A		RSRC1-related disorder	Likely benign (Aug 09, 2022)
3-158122213-C-T		Autism	Pathogenic (-)
3-158122233-A-G			Likely benign (Sep 01, 2022)
3-158122274-C-A		Inborn genetic diseases	Uncertain significance (May 23, 2023)
3-158122276-C-T		Inborn genetic diseases	Uncertain significance (Dec 06, 2023)
3-158122299-G-A		Inborn genetic diseases	Pathogenic (Dec 01, 2020)
3-158123867-C-T		Intellectual developmental disorder, autosomal recessive 70	Uncertain significance (Sep 06, 2019)
3-158123868-G-T		Inborn genetic diseases	Uncertain significance (Dec 02, 2022)
3-158123876-C-T		Intellectual developmental disorder, autosomal recessive 70	Pathogenic (Oct 06, 2023)
3-158123895-C-T		Inborn genetic diseases	Uncertain significance (May 08, 2023)
3-158123901-GC-AA		Intellectual developmental disorder, autosomal recessive 70	Uncertain significance (Sep 22, 2024)
3-158123933-A-G		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
3-158123936-G-A		Inborn genetic diseases	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RSRC1	protein_coding	protein_coding	ENST00000295930	9	439876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000745	0.982	125711	0	29	125740	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0946	176	180	0.980	0.0000108	2124
Missense in Polyphen		36	42.971	0.83777		683
Synonymous	-1.10	66	55.6	1.19	0.00000260	632
Loss of Function	2.12	10	20.3	0.493	0.00000126	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000201	0.000193
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in pre-mRNA splicing. Involved in both constitutive and alternative pre-mRNA splicing. May have a role in the recognition of the 3' splice site during the second step of splicing. {ECO:0000269|PubMed:15798186}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.280
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.379
• hipred: N
• hipred_score: 0.390
• ghis: 0.663

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rsrc1

Gene ontology

• Biological process: alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;protein phosphorylation;nucleocytoplasmic transport;RNA splicing;response to antibiotic
• Cellular component: nucleus;cytoplasm;nuclear speck
• Molecular function: protein binding